AMBER Archive (2009)

Subject: Re: [AMBER] MD snapshots of most probable protein conformations in Amber

From: Renata KWIECIEN (Renata.Kwiecien_at_univ-nantes.fr)
Date: Wed Nov 18 2009 - 07:39:52 CST

Check "cluster" option in MMTSB.
http://blue11.bch.msu.edu/mmtsb/Main_Page

Best regards,
Renata

> Actually the question is about how to generate protein conformations
> ensemble and then to select the most probable conformations.
> It s possible to generate receptors ensemble using namd and it should be
> possible by using amber, but I need let s say 30 most probable
> conformations of proteins which have the highest occurence rate in the
> 5-10 nanosecond trajectory.
>
> Is it possible to do it by ptraj for example?
>
> Best regards,
> Andrew
>
> 12.11.09, 08:30, "Adrian Roitberg" <roitberg_at_qtp.ufl.edu>:
>
>> I am not sure, but I believe that Andy Mc Cammon's group has implemented
>> this setup in their own web site, extending it from namd as in the paper
>> you mentioned, to amber now.
>> Adrian
>> Andrew Voronkov wrote:
>> > Dear Amber users,
>> > are there any tutorials online on usage of some analogs of relaxed
>> complex scheme, described here:
>> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516539/?tool=pubmed#aff-info
>> >
>> > I mean optimization of MD trajectory snapshots and usage of most
>> probable protein conformations from MD trajectories in Amber?
>> >
>> >
>> > Best regards,
>> > Andrey
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER_at_ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>
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